The judge is merely pointing out the obvious that science cannot detect the supernatural, thus is "atheistic". By definition, science deals with the natural world, therefore anything it can detect and measure is a part of the natural world, I.E. "atheistic".
That situation could change when the first scientist detects, or describes a method to determine the nature of God. That scientist will become the most famous in history too, so don't tell me that all scientists are anti-God and wouldn't attempt such work.
You talk out of both sides of your mouth. First you say science is by nature atheistic, then you suggest a scenario at some point down the road when a scientist might detect, or describe a method to determine the nature of God.